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Ch. 11 - DNA Replication and Recombination
Chapter 11, Problem 27

DNA polymerases in all organisms add only 5' nucleotides to the 3' end of a growing DNA strand, never to the 5' end. One possible reason for this is the fact that most DNA polymerases have a proofreading function that would not be energetically possible if DNA synthesis occurred in the 3' to 5' direction. Consider the information in your sketch and speculate as to why proofreading would be problematic.

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1
Understand that DNA polymerases synthesize DNA in the 5' to 3' direction, adding nucleotides to the 3' end of the growing strand.
Recognize that DNA polymerases have a proofreading function, which involves removing incorrectly paired nucleotides and replacing them with the correct ones.
Consider the energy requirements for proofreading: in the 5' to 3' direction, the energy for adding a nucleotide comes from the hydrolysis of the triphosphate group of the incoming nucleotide.
Speculate that if DNA synthesis occurred in the 3' to 5' direction, removing an incorrect nucleotide would leave a monophosphate at the 5' end, lacking the necessary energy to add a new nucleotide.
Conclude that the lack of available energy for nucleotide addition after proofreading in the 3' to 5' direction would make the process energetically unfavorable, thus explaining why DNA polymerases synthesize in the 5' to 3' direction.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

DNA Polymerase Function

DNA polymerases are enzymes responsible for synthesizing new DNA strands by adding nucleotides to the growing chain. They can only add nucleotides to the 3' end of the strand, which means that DNA synthesis occurs in a 5' to 3' direction. This unidirectional synthesis is crucial for maintaining the integrity and accuracy of DNA replication.
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Proofreading Mechanism

Proofreading is a critical function of DNA polymerases that allows them to correct errors during DNA synthesis. When an incorrect nucleotide is added, the enzyme can detect the mismatch and remove the erroneous nucleotide before continuing synthesis. This mechanism relies on the enzyme's ability to reverse its direction temporarily, which would be energetically inefficient if DNA synthesis occurred in the 3' to 5' direction.
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Energetics of DNA Synthesis

The energetics of DNA synthesis refers to the energy requirements for adding nucleotides to a growing DNA strand. The process is driven by the hydrolysis of nucleoside triphosphates (NTPs), which release energy when incorporated into the DNA. If DNA polymerases were to synthesize DNA in the 3' to 5' direction, it would complicate the energy dynamics and potentially hinder the proofreading process, making it less efficient.
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Related Practice
Textbook Question
Assume a hypothetical organism in which DNA replication is conservative. Design an experiment similar to that of Taylor, Woods, and Hughes that will unequivocally establish this fact. Using the format established in Figure 11.5, draw sister chromatids and illustrate the expected results establishing this mode of replication.
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Textbook Question
At the end of the short arm of human chromosome 16 (16p), several genes associated with disease are present, including thalassemia and polycystic kidney disease. When that region of chromosome 16 was sequenced, gene-coding regions were found to be very close to the telomere-associated sequences. Could there be a possible link between the location of these genes and the presence of the telomere-associated sequences? What further information concerning the disease genes would be useful in your analysis?
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Textbook Question
DNA polymerases in all organisms add only 5' nucleotides to the 3' end of a growing DNA strand, never to the 5' end. One possible reason for this is the fact that most DNA polymerases have a proofreading function that would not be energetically possible if DNA synthesis occurred in the 3' to 5' direction. Sketch the reaction that DNA polymerase would have to catalyze if DNA synthesis occurred in the 3' to 5' direction.
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Textbook Question
Assume that the sequence of bases shown below is present on one nucleotide chain of a DNA duplex and that the chain has opened up at a replication fork. Synthesis of an RNA primer occurs on this template starting at the base that is underlined. If the RNA primer consists of eight nucleotides, what is its base sequence?
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Textbook Question
Assume that the sequence of bases shown below is present on one nucleotide chain of a DNA duplex and that the chain has opened up at a replication fork. Synthesis of an RNA primer occurs on this template starting at the base that is underlined. In the intact RNA primer, which nucleotide has a free 3'-OH terminus? 3'.......GGCTACCTGGATTCA....5'
472
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Textbook Question
Reiji and Tuneko Okazaki conducted a now classic experiment in 1968 in which they discovered a population of short fragments synthesized during DNA replication. They introduced a short pulse of ³H-thymidine into a culture of E. coli and extracted DNA from the cells at various intervals. In analyzing the DNA after centrifugation in denaturing gradients, they noticed that as the interval between the time of ³H-thymidine introduction and the time of centrifugation increased, the proportion of short strands decreased and more labeled DNA was found in larger strands. What would account for this observation?
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